Expanding on this idea, MetaOmGraph (metnetdb.org) enables you to do
correlations with very large datasets (thousands of chips) on either
already-created files of data from Arabidopsis or several other organisms,
or on your own microarray or metabolomic data files. Alternately, you can
create files from ArrayExpress public microarray data.

There are multiple options for visualization, ordering, and sorting the
types of experimental conditions you want to include in the correlation.